renamed cython_distance module -> cython_profiles

5 files changed, 38 insertions, 39 deletions

diff --git a/pyspike/cython/cython_distance.pyx b/pyspike/cython/cython_profiles.pyx
index 6ee0181..59a8d30 100644
--- a/pyspike/cython/cython_distance.pyx
+++ b/pyspike/cython/cython_profiles.pyx
@@ -3,9 +3,9 @@
 #cython: cdivision=True
 
 """
-cython_distances.pyx
+cython_profiles.pyx
 
-cython implementation of the isi- and spike-distance
+cython implementation of the isi-, spike- and spike-sync profiles
 
 Note: using cython memoryviews (e.g. double[:]) instead of ndarray objects
 improves the performance of spike_distance by a factor of 10!
@@ -20,11 +20,11 @@ Distributed under the BSD License
 To test whether things can be optimized: remove all yellow stuff
 in the html output::
 
-  cython -a cython_distance.pyx
+  cython -a cython_profiles.pyx
 
 which gives::
 
-  cython_distance.html
+  cython_profiles.html
 
 """
 
@@ -40,10 +40,10 @@ ctypedef np.float_t DTYPE_t
 
 
 ############################################################
-# isi_distance_cython
+# isi_profile_cython
 ############################################################
-def isi_distance_cython(double[:] s1, double[:] s2,
-                        double t_start, double t_end):
+def isi_profile_cython(double[:] s1, double[:] s2,
+                       double t_start, double t_end):
 
     cdef double[:] spike_events
     cdef double[:] isi_values
@@ -173,10 +173,10 @@ cdef inline double isi_avrg_cython(double isi1, double isi2) nogil:
 
 
 ############################################################
-# spike_distance_cython
+# spike_profile_cython
 ############################################################
-def spike_distance_cython(double[:] t1, double[:] t2,
-                          double t_start, double t_end):
+def spike_profile_cython(double[:] t1, double[:] t2,
+                         double t_start, double t_end):
 
     cdef double[:] spike_events
     cdef double[:] y_starts
@@ -342,7 +342,7 @@ def spike_distance_cython(double[:] t1, double[:] t2,
 
 
 ############################################################
-# coincidence_python
+# get_tau
 ############################################################
 cdef inline double get_tau(double[:] spikes1, double[:] spikes2,
                            int i, int j, double max_tau):
@@ -364,10 +364,10 @@ cdef inline double get_tau(double[:] spikes1, double[:] spikes2,
     
 
 ############################################################
-# coincidence_cython
+# coincidence_profile_cython
 ############################################################
-def coincidence_cython(double[:] spikes1, double[:] spikes2,
-                       double t_start, double t_end, double max_tau):
+def coincidence_profile_cython(double[:] spikes1, double[:] spikes2,
+                               double t_start, double t_end, double max_tau):
 
     cdef int N1 = len(spikes1)
     cdef int N2 = len(spikes2)
diff --git a/pyspike/isi_distance.py b/pyspike/isi_distance.py
index 8b1e9bf..164378d 100644
--- a/pyspike/isi_distance.py
+++ b/pyspike/isi_distance.py
@@ -31,18 +31,18 @@ def isi_profile(spike_train1, spike_train2):
 
     # load cython implementation
     try:
-        from cython.cython_distance import isi_distance_cython \
-            as isi_distance_impl
+        from cython.cython_profiles import isi_profile_cython \
+            as isi_profile_impl
     except ImportError:
         print("Warning: isi_distance_cython not found. Make sure that PySpike \
 is installed by running\n 'python setup.py build_ext --inplace'!\n \
 Falling back to slow python backend.")
         # use python backend
         from cython.python_backend import isi_distance_python \
-            as isi_distance_impl
+            as isi_profile_impl
 
-    times, values = isi_distance_impl(spike_train1.spikes, spike_train2.spikes,
-                                      spike_train1.t_start, spike_train1.t_end)
+    times, values = isi_profile_impl(spike_train1.spikes, spike_train2.spikes,
+                                     spike_train1.t_start, spike_train1.t_end)
     return PieceWiseConstFunc(times, values)
 
 
diff --git a/pyspike/spike_distance.py b/pyspike/spike_distance.py
index 499ab77..3567585 100644
--- a/pyspike/spike_distance.py
+++ b/pyspike/spike_distance.py
@@ -31,20 +31,20 @@ def spike_profile(spike_train1, spike_train2):
 
     # cython implementation
     try:
-        from cython.cython_distance import spike_distance_cython \
-            as spike_distance_impl
+        from cython.cython_profiles import spike_profile_cython \
+            as spike_profile_impl
     except ImportError:
-        print("Warning: spike_distance_cython not found. Make sure that \
+        print("Warning: spike_profile_cython not found. Make sure that \
 PySpike is installed by running\n 'python setup.py build_ext --inplace'!\n \
 Falling back to slow python backend.")
         # use python backend
         from cython.python_backend import spike_distance_python \
-            as spike_distance_impl
+            as spike_profile_impl
 
-    times, y_starts, y_ends = spike_distance_impl(spike_train1.spikes,
-                                                  spike_train2.spikes,
-                                                  spike_train1.t_start,
-                                                  spike_train1.t_end)
+    times, y_starts, y_ends = spike_profile_impl(spike_train1.spikes,
+                                                 spike_train2.spikes,
+                                                 spike_train1.t_start,
+                                                 spike_train1.t_end)
     return PieceWiseLinFunc(times, y_starts, y_ends)
 
 
diff --git a/pyspike/spike_sync.py b/pyspike/spike_sync.py
index 7d429e4..107734d 100644
--- a/pyspike/spike_sync.py
+++ b/pyspike/spike_sync.py
@@ -36,24 +36,23 @@ def spike_sync_profile(spike_train1, spike_train2, max_tau=None):
 
     # cython implementation
     try:
-        from cython.cython_distance import coincidence_cython \
-            as coincidence_impl
+        from cython.cython_profiles import coincidence_profile_cython \
+            as coincidence_profile_impl
     except ImportError:
         print("Warning: spike_distance_cython not found. Make sure that \
 PySpike is installed by running\n 'python setup.py build_ext --inplace'!\n \
 Falling back to slow python backend.")
         # use python backend
         from cython.python_backend import coincidence_python \
-            as coincidence_impl
+            as coincidence_profile_impl
 
     if max_tau is None:
         max_tau = 0.0
 
-    times, coincidences, multiplicity = coincidence_impl(spike_train1.spikes,
-                                                         spike_train2.spikes,
-                                                         spike_train1.t_start,
-                                                         spike_train1.t_end,
-                                                         max_tau)
+    times, coincidences, multiplicity \
+        = coincidence_profile_impl(spike_train1.spikes, spike_train2.spikes,
+                                   spike_train1.t_start, spike_train1.t_end,
+                                   max_tau)
 
     return DiscreteFunc(times, coincidences, multiplicity)
 
diff --git a/setup.py b/setup.py
index 289d521..d687240 100644
--- a/setup.py
+++ b/setup.py
@@ -22,7 +22,7 @@ else:
     use_cython = True
 
 if os.path.isfile("pyspike/cython/cython_add.c") and \
-   os.path.isfile("pyspike/cython/cython_distance.c"):
+   os.path.isfile("pyspike/cython/cython_profiles.c"):
     use_c = True
 else:
     use_c = False
@@ -33,13 +33,13 @@ ext_modules = []
 if use_cython:  # Cython is available, compile .pyx -> .c
     ext_modules += [
         Extension("pyspike.cython.cython_add", ["pyspike/cython/cython_add.pyx"]),
-        Extension("pyspike.cython.cython_distance", ["pyspike/cython/cython_distance.pyx"]),
+        Extension("pyspike.cython.cython_profiles", ["pyspike/cython/cython_profiles.pyx"]),
     ]
     cmdclass.update({'build_ext': build_ext})
 elif use_c:  # c files are there, compile to binaries
     ext_modules += [
         Extension("pyspike.cython.cython_add", ["pyspike/cython/cython_add.c"]),
-        Extension("pyspike.cython.cython_distance", ["pyspike/cython/cython_distance.c"]),
+        Extension("pyspike.cython.cython_profiles", ["pyspike/cython/cython_profiles.c"]),
     ]
 # neither cython nor c files available -> automatic fall-back to python backend
 
@@ -78,7 +78,7 @@ train similarity',
         'Programming Language :: Python :: 2.7',
     ],
     package_data={
-        'pyspike': ['cython/cython_add.c', 'cython/cython_distance.c'],
+        'pyspike': ['cython/cython_add.c', 'cython/cython_profiles.c'],
         'test': ['Spike_testdata.txt']
     }
 )